Tertiary hydrogen bonds in the solution structure of transfer RNA

Probing the conformation of human tRNA(3)(Lys) in solution by NMR

Human tRNA(3)(Lys) acts as a primer for the reverse transcription of human immunodeficiency virus genomic RNA. To form an initiation complex with genomic RNA, tRNA(3)(Lys) must reorganize its secondary structure. To provide a starting point for mechanistic studies of the formation of the initiation complex, we here present solution NMR investigations of human tRNA(3)(Lys). We use a straightforward set of NMR experiments to show that tRNA(3)(Lys) adopts a standard transfer ribonucleic acid tertiary structure in solution, and that Mg(2+) is required for this folding. The results underscore the power of NMR to reveal rapidly the conformation of RNAs.

Characterization of the secondary structure and melting of a self-cleaved RNA hammerhead domain by 1H NMR spectroscopy

We have completely assigned the extreme low-field ring-NH nuclear magnetic resonance spectrum of a self-cleaving RNA in the absence of magnesium ions by experiments involving sequential Overhauser enhancements between adjacent base pairs. These assignments substantiate the hammerhead secondary folding model proposed by Symons and co-workers for this class of self-cleaving RNA [Hutchins, C. J., Rathjen, P. D., Forster, A. C., & Symons, R. H. (1986) Nucleic Acids Res. 14, 3627-3640; Forster, A. C. & Symons, R. H. (1987) Cell 49, 211-220; Kneese, P., & Symons, R. H. (1987) in Viroids and Viroid-like Pathogens (Semancick, J. S., Ed.) pp 1-47, CRC Press, Boca Raton, FL]. No resonances due to tertiary base pairs could be identified in the low-field spectrum, and addition of MgCl2 to the sample did not produce additional resonances in this region of the spectrum.

Pulsed FT-NMR double resonance studies of yeast tRNAPhe: specific nuclear Overhauser effects and reinterpretation of low temperature relaxation data

Cross-relaxation effects are demonstrated between the imino protons and other protons in yeast tRNAPhe and H2O. A detailed examination has been made of the observed relaxation rate of the proton resonance at 11.8 ppm from DSS as a function of the D2O content in the solvent. This result, as well as the size and number of observed nuclear Overhauser effects, suggests that dipolar magnetization transfer between solvent H2O, amino, imino, and other tRNA protons may dominate the relaxation processes of the imino protons at low temperature. At higher temperatures the observed relaxation rate is dominated by chemical exchange. The selective nuclear Overhauser effects are shown to be an important aid in resonance assignments. By these means we were able to identify tow protons from the wobble base pair GU4 at 11.8 ppm and 10.4 ppm.

Demonstration of a tertiary interaction in solution between the extra arm and the D-stem in two different transfer RNA's by NMR

According to the X-ray structure of yeast tRNAPhe at 2.5 A resolution, a hydrogen bond is formed between m7G46 and G22. By removal of this m7G46-residue we demonstrate that this interaction is present in solution as well. Comparison of the 1H 360 MHz NMR spectra of intact yeast tRNAPhe and its m7G-excised derivative locates the position of this tertiary H-bond at 12.5 ppm downfield from DSS. Additional evidence for the presence of this interaction in solution comes from a comparison of 1H NMR spectra of E. coli tRNAf1Met and E. coli tRNAf3Met, which differ only in a single position in the extra arm. In tRNAf3Met residue 47 is a m7G-residue, whereas in tRNAf3Met it is A, resulting in the absence of the m7G47 - G23 - C13 triple interaction, characteristic of tRNAf1Met. The resonance position of this tertiary interaction in tRNAf1Met is located around -13.6 ppm, a chemical shift difference of 1.1 ppm with respect to the position observed for tRNAPhe. The origin of this chemical shift difference is discussed in relation to the structure of their respective augmented D-helices.

Nonintercalative binding of ethidium bromide to nucleic acids: crystal structure of an ethidium--tRNA molecular complex

X-ray diffraction studies at 4.5-A resolution on crystals of a complex of ethidium bromide and yeast phenylalanine tRNA reveal a nonintercalative model of binding of the ethidium within the tertiary structure. This is contrary to the expected interacalative binding to the double-helical regions.

An NMR study of the exchange rates for protons involved in the secondary and tertiary structure of yeast tRNA Phe

Solvent exchange rates of all the protons of yeast tRNAphe resonating in the lowfield NMR region (-11 to-15 ppm from DSS) have been measured by saturation-recovery long-pulse Fourier transform NMR. All these protons in yeast tRNAphe are in the fast exchange limit with H2O relative to their intrinsic longitudinal relaxation processes. Most rates show very little temperature dependence; however, tertiary base pair protons are preferentially destabilized in the absence of Mg++ at higher temperatures. The measured exchange rates are between 2 and 125 sec-1 for a temperature range from 10 degrees C to 45 degrees C and MgCl2 concentrations between 0 and 15 mM.

High-resolution nuclear magnetic resonance determination of transfer RNA tertiary base pairs in solution. 1. Species containing a small variable loop

Eight class I tRNA species have been purified to homogeneity and their proton nuclear magnetic resonance (NMR) spectra in the low-field region (-11 to -15 ppm) have been studied at 360 MHz. The low-field spectra contain only one low-field resonance from each base pair (the ring NH hydrogen bond) and hence directly monitor the number of long-lived secondary and tertiary base pairs in solution. The tRNA species were chosen on the basis of their sequence homology with yeast phenylalanine tRNA in the regions which form tertiary base pairs in the crystal structure of this tRNA. All of the spectra show 26 or 27 low-field resonances approximately 7 of which are derived from tertiary base pairs. These results are contrary to previous claims that the NMR spectra indicate the presence of resonances from secondary base pairs only, as well as more recent claims of only 1-3 tertiary resonances, but are in good agreement with the number of tertiary base pairs expected in solution based on the crystal structure. The tertiary base pair resonances are stable up to at least 46 degrees C. Removal of magnesium ions causes structural changes in the tRNA but does not result in the loss of any secondary or tertiary base pairs.

High-resolution nuclear magnetic resonance determination of transfer RNA tertiary base pairs in solution. 2. Species containing a large variable loop

The number of base pairs in the solution structure of several class III D3VN tRNA species from E. coli has been determined by analyzing the number of low-field (-15 to -11 ppm) proton resonances in their nuclear magnetic resonance spectra at 360 MHz. Contrary to previous reports indicating the absence of tertiary resonances, all the spectra exhibit the expected number of secondary base pair resonances plus approximately ten extra resonances derived from tertiary base pairs in the three-dimensional folding of these molecules. The possible origins of some of these tertiary resonances are discussed; none of the spectra exhibits the characteristic resonance of the 8-14 tertiary base pair seen in class I D4V5 tRNA spectra.

1H NMR studies of transfer RNA III: the observed and the computed spectra of the hydrogen-bonded NH resonances of baker's yeast transfer-RNA Phe

The hydrogen-bonded NH resonances of Baker's yeast tRNAphe in H2O solution with Mg++ have been measured by a 360 MHz spectrometer at 23 degrees C. Totally, fifteen peaks and one shoulder can be resolved which represent 25 +/- 1 protons. Based on the refined atomic coordinates of the tRNAphe in the orthorhombic crystal, on the recent advances in the distance dependence of the ring-current magnetic field effects and on the adopted values for the isolated hydrogen-bonded NH resonances, a computed spectrum consisting of 23 protons was constructed. A quantitative comparison by computer was made between the computed spectrum and the spectrum simulated from the observed spectrum. These two spectra are closely similar but not identical. We suggest that the conformation of yeast tRNAphe in aqueous solution is closely similar but not identical to that found in the crystal, especially in the T psi C region and D region. Also the NH resonances in 3-4 proposed hydrogen bonds (most likely for tertiary structure) may exchange very rapidly in aqueous solution.

RNA structure

This review is concerned primarily with the physical structure and changes in the structure of RNA molecules. It will be evident that we have not attempted comprehensive coverage of what amounts to a vast literature. We have tried to stay away from particular areas that have been recently reviewed elsewhere. Citations to and information from them are included, however, so that access to the literature is available. Much of what we treat in depth deals with the crystal structures and solution behaviour of model RNA compounds, including synthetic polymers and molecular fragments such as dinucleoside phosphates. Sequence data on natural RNA are cited, but not in detail. Similarly, apart from tRNA, natural RNAs the structural determinations of which are presently not so far advanced, are not dwelt upon. We have tried to present in detail the available structural data with scaled drawings that permit facile comparisons of molecular geometries.

Hydrogen-bonded protons in the tertiary structure of yeast tRNAPhe in solution

Temperature-dependent lowfield proton magnetic resonance spectra of yeast tRNAPhe were recorded between 10 and 15 parts per million. Seven resonances of hydrogen-bonded protons disappeared reversibly under two sets of conditions where the selective broadening of tertiary structure resonances were predicted by temperature jump experiments. The seven resonances were assigned to the seven tertiary hydrogen bonds expected between 10 and 15 parts per million from the crystal structure of yeast tRNAPhe. Some of the non-Watson-Crick base pairs have unusual unshifted standard chemical shifts after the ring current contributions calculated from the crystal coordinates were subtracted. The differences of the chemical shifts of homologous tertiary structure base pairs in Escherichia coli tRNAfMet and yeast tRNAPhe give experimental evidence for details of the conformational differences postulated by model building on the basis of the x-ray coordinates of yeast tRNAPhe and sequence homologies.

An NMR approach to tRNA tertiary structure in solution

Atomic coordinates of E. Coli tRNA1Val have been generated from the X-ray crystal structure of Yeast tRNAPhe by base substitution followed by idealization...

Proton magnetic resonance spectra of tRNA-Met-f from Thermus thermophilus

220 MHz proton magnetic resonance spectra of tRNAs in bulk and tRNA-Met-f from Thermus thermophilus have been measured and compared with those of tRNAs from E. coli. Temperature dependences and chemical shift positions of the bulk tRNAs are well explained by the difference in their GC contents. It is known that the base sequence of the double helical regions in the cloverleaf structure of T. thermophilus tRNA-Met-f is different from that of E. coli tRNA-Met-f only at two positions in TpsiCarm; one more C:G pair is contained instead of a U:G pair of E. coli tRNA-Met-f and a C:G pair of E. coli is replaced by a G:C pair. In spite of the resembrance in the base sequences, nmr patterns around 13 ppm are fairly different from each other. The difference is discussed in relation with their tertiary structures and with the origin of chemical shift displacements.

The iminoproton NMR spectrum of yeast tRNA-Phe predicted from crystal coordinates

The ring current effects on the base paired iminoprotons in yeast tRNA-Phe have been calculated from crystal coordinates. The results in conjunction with independently determined intrinsic positions of the iminoprotons in various base pairs enable us to predict the low field NMR spectrum of yeast tRNA-Phe. It turns out that the calculated NMR spectra are very sensitive to slight changes in structure. Moreover the crystal and solution structure are identical as far as the present methods go.

The kinetics of bisulphite modification of reactive residues in E. coli tRNA2Phe

E coli tRNA2Phe was modified at 25 degrees C with 3M sodium bisulphite, pH6.0, for periods of up to 48 hours, Three cytadinine residues, at position 17, 74 and 75 from the 5' end were each deaminated to uridine. The 2-methylthio-N6-isopentenyl adenosine at position 37 formed a 1:1 bi-sulphite addition product which was stable to alkaii. No other residues were permanently modified. The rate of modification of each residue was first order with respect to remaining unmodified nucleotide, the time of half reaction, t1/2, being different for each residue. C17 reaction reacted at twice the rate of cytidine in PolyC, indicating that it occupied a very exposed position in the tRNA.

Physical studies of denatured tRNA2Glu from Escherichia coli

We have examined the 270 MHz nuclear magnetic resonance spectrum and relaxation kinetic behavior of tRNA2Glu (E. coli) in the absence of Mg++, a condition which produces an inactive form of this tRNA. The results show that the denatured form has about five fewer proton resonances in the region from -12 to -15 ppm. Relaxation kinetic measurements reveal that the denatured conformer contains three separately melting helices. The results support a model in which the tertiary structure and dihydrouridine helix characteristic of the native form are unfolded in the denatured state, and are replaced by an altered tertiary structure. The acceptor stem, anticodon, and TpsiC helices are intact in this model for the denatured conformation. The optical changes that accompany melting of the denatured tertiary structure are faster than 10 musec.

CD spectra of 5-methyl-2-thiouridine in tRNA-Met-f from an extreme thermophile

5-Methyl-2-thiouridine (S) in tRNA-Met-f from an extreme thermophile is located in the TpsiC region, replacing T, and has a positive CD band centered at 310 nm. Upon heating, the profiles of the change in this band were similar to the UV melting profiles of the change monitored at 260 nm. This strongly suggests a close relation between heat denaturation of the tRNA and the conformation of the S base. Oligonucleotides containing S showed negative CD bands at 320-330 nm, like the monomer S itself, but when the 3'-2/5 fragment containing S formed a complex with the complementary 5'-3/5 fragment, a positive CD band appeared at 310 nm. These results suggest that combination of the TpsiC loop containing S with the hU loop is necessary for the positive band of S at 310 nm. S may serve to strengthen the association of the TpsiC loop with the hU loop in tRNA of the thermophile.